Metroid Prime
by Wunderwaffen
Summary: This is a novelization of Metroid Prime. It contains things and even a character that wasn't in the actual game. I hope you enjoy it.
1. Chapter 1

Prologue

_Unidentified distress beacon has been tracked to a derelict space vessel in orbit above Tallon IV._

Samus Aran looked around at the seemingly deserted frigate Orpheon. At least the docking bay was deserted. Samus had yet to check out the rest of the vessel, which was what she was about to do.

After deactivating a force field, she noticed that the next set of force field controls were offline. Turning on her new Scan Visor, she scanned a panel nearby. _Force field activation switches are now online._

Samus deactivated the second force field and walked up the ramp. She opened the door at the top and went into the access corridor. There were holographic icons on the left wall that she could scan. One of them was flashing. She scanned the first two and they said, _Deck Gamma. Reactor core and propulsion. Current status: environment normal._ And _Deck Beta. Biotech research. Current status: environment normal._ When she scanned the one that was flashing, it said, _Deck Alpha. Emergency evacuation area. Current status: environment unstable._ Samus realized something was definitely going on there.

She opened the door to the air lock, where bits of metal and a couple of parasite carcasses were floating around. Samus scanned the nearby panel to repressurize the airlock. The ship's air flooded into the room and the bits of metal and parasites clattered to the floor as the artificial gravity kicked in. Samus moved on to the Deck Alpha access corridor and shot open the door to the emergency evacuation area.

Samus stared in shock at what she saw. A huge creature was lying dead on the floor, wreathed in flame. Parasites scuttled here and there, and everywhere there were dead Space Pirates. Samus scanned one. _Morphology: Space Pirate. Status: death caused by a severing of the spinal cord._ The scan of another dead Pirate said:_ Morphology: Space Pirate. Status: death caused by acidic burns to body. Chemical type unknown._ Another scan said: _Morphology: Space Pirate. Status: death caused by severe flame damage to exoskeleton._ Samus then scanned the big thing that lay dead in the center of the room, starting with its body. _Morphology: Unknown. Info High levels of radiation detected._ Samus scanned the creature's head next. _Analysis shows incredibly large muscle structures surrounding the jaw area. Fluid sacs containing acid are also detected._ Scans of the tail yielded similar results. _Tail section possesses a mouthlike orifice. Most likely used for birthing offspring._

Samus scanned one of several hexagonal shaped portholes in the far wall. _Escape pod entrance. The vessel has already been jettisoned. Evacuation occurred six hours prior to your arrival._

Samus went thru the door on the far side and found the corridor blocked by rubble, which she destroyed with her Charge Beam. She then scanned a corpse underneath. _Morphology: Space Pirate. Status: Death caused by excessive blunt trauma to cranium._ Samus chuckled. "Well I should say so!"

After downloading the map of the ship, she continued on. When she came to the biotech research area 2, she saw that two of the three huge stasis tanks built to house Parasite Queen specimens were broken open and their contents were nowhere to be seen. Obviously one of them was the same one she saw dead on the floor of the emergency evacuation area, but what about the other one?

Samus soon arrived at the biohazard containment room. In a stasis tank was another Parasite Queen. Samus scanned it. _Morphology: Unknown. Info This specimen has been horribly mutated. There are no life readings._ Samus scanned a computer nearby and got the first Pirate Data entry in her quest.

_ Zebes has fallen. All ground personnel are presumed dead, either killed by the Hunter clad in metal or in the subsequent destruction of the underground facilities. Our research frigates Orpheon, Siracus, and Vol Paragon were in orbit at zero hour and managed to retreat. Frigate Orpheon is now docked at vortex outpost. Orpheon's cargo appears to have a 100% survival rate; Metroids are healthy but on restricted feeding schedules due to uncertain supply status. We are ready to begin research on the Metroids and other promising life forms. Security status remains at Code Blue; no signs of pursuit from the Hunter._

Samus traveled thru the ship until she reached Reactor Access. There she found more bodies. _Morphology: Space Pirate. Status: Dead. This creature looks like it struggled to get thru this door._

_ Morphology: Space Pirate. Status: Death caused by severe lacerations. Subject looks like it has been partially eaten._

In the Reactor Core, Samus found more bodies. _Analysis detects large amounts of blood missing from the carcasses. These bodies may have been used for nourishment. Pattern consistent with predator behavior._

Samus approached the reactor. Suddenly she heard a clamoring sound. She looked up and saw something huge enter the reactor field. It was without question the second Parasite Queen.

_Morphology: Parasite Queen: Parasite female, genetically enhanced by unknown means. A weak spot has been detected in this creature's mouth: use your auto-targeting to acquire this new target! Scans indicate the presence of a potent mutagen, origins unknown. Creature exhibits the ability to fire weapon-grade blasts of energy from its mouth, a trait not present in the standard Parasite genome. It appears that the Space Pirates have begun a bioengineering program, with considerable results._

The Queen was less resilient than she seemed. After blasting it for a few minutes, the metal plate beneath it gave way, and it got sucked into the reactor. An explosion followed by tendrils of energy was the result. An electronic voice said, "Evacuate immediately. Evacuate immediately." A message on Samus's visor said, _Reactor core critical! Evacuate immediately!_

Samus hightailed it out of there, escaping thru the ventilation shafts, until she reached Biotech Research Area 2. There, Samus heard a familiar sound and looked up. "Ridley. So you are alive. Well I'll soon change that." Ridley stared down at her with a smug expression on his face, then broke thru the ceiling and flew out of sight. Samus swung across the gap with her Grapple Beam, then scanned a nearby panel. _Subject: Meta Ridley. Begin umbilical retraction._ "So he's Meta Ridley now, is he?" Samus said to herself.

Samus scanned the elevator to take her to the air lock, but a noise caused her to stop. She turned around just in time to see several huge pieces of metal slam into her, hurling her against the wall and destroying her Varia Suit. As Samus went up the elevator, a message appeared on her visor. _Varia Suit malfunction. Morph Ball Bomb malfunction. Charge beam malfunction. Missile malfunction. Morph Ball Malfunction. Grapple Beam malfunction._ Samus realized to her horror that she now had only the Power Suit, Power Beam, Combat Visor and Scan Visor, making her virtually defenseless!

The Power Suit

Upon arrival at the Docking bay, Samus jumped into her ship and saw Meta Ridley flying out. Samus pursued him and together they descended towards Tallon IV.

_Tracking on enemy target has been lost. Ground-based recon required. Begin landing sequence._


	2. Chapter 2

Chapter 1

Planetfall

Samus made planetfall in the Tallon Overworld, that part of the planet that is a huge and beautiful rainforest, albeit one where it rains 24/7. After scanning various interesting things Samus surveyed the landing site.

There were at least four doors in the landing site, but thanks to the incident on the research frigate Orpheon, only one was currently reachable. Samus went thru the door into a small cavern. After killing a bunch of beetles, she went thru the door in the cavern and found herself in Tallon Canyon. It was a beautiful place, with the trees and the rain.

One of the first things to catch Samus's eye, however, was something she instantly recognized, and blanched when she saw it. _Is that a…_ She switched to the Scan Visor and scanned it. _These large branches have been forcibly intertwined, forming what looks to be a bridge structure._ The last time Samus had seen such a bridge was in the ruins of the place where she grew up. _A Chozo colony!_ And there was more. Samus scanned the u-shaped surface underneath the bridge. Definitely a half-pipe for the Boost Ball. Both bridge and half-pipe were irrefutable evidence of Chozo habitation.

Samus opened the door beyond the half-pipe and sprinted thru the narrow hallway beyond. Upon going thru the door at the end of the hallway, Samus found herself in a small, dimly lit room with an elevator. Samus scanned the panel beside the elevator. _Access to Chozo City East granted. Please step into the hologram._ Samus stepped into the hologram and ascended to the Chozo City.

Upon arrival, Samus exited the elevator room, ran out into the open, and stopped… from the horror of what she saw.

Stone pillars. Broken. Stone walls. Cracked and crumbling and overgrown. Dust. Wind. Silence.

Samus dispatched two beetles and took off her helmet. The air was dry. She looked around and then… she started to cry. This was no city, but a ruin. There was not a sight nor sound of any living thing. The whole place was falling apart.

Samus knew that whatever had wiped out the Chozo here and reduced their colony to such a state was not the Space Pirates. No, Samus felt a malevolent force here, something far more terrible than the Space Pirates themselves. This was more like the one whose fault it was that the Pirates were as bad as they were… the malevolent, power-crazed Mother Brain.

Samus considered whether this had something to do with it. No matter where she might be, the Mother Brain would always be the same within. Nothing could change that. As an entity it was power mad and pure evil, a being of enormous strength forever teetering on the edge of insanity. She stood for everything Samus hated.

She found herself hoping that this actually was the work of the Mother Brain. It would give Samus Aran the opportunity to remove from the civilized galaxy the work of one of the greatest abominations that ever existed. If it didn't remove her first, of course.

Suddenly her visor told her that there was seismic activity coming from a room called the Hive Totem. Samus decided she would head toward it.

Samus noticed a shimmering patch of wall above the door leading out of the entrance. She scanned it.

_ A new Chozo Lore entry has been downloaded to your logbook. Chozo script translated._

_ At the highest point of our city lies the fountain, a wellspring of pure water that flows throughout our civilization. It is the jewel of the Chozo, the lifegiver, and yet it's waters speak of a clouded future. As we come to understand the paths of time and space more clearly, we have begun to glimpse rough tatters of past and future, glittering behind reality like soft lights behind a curtain. We have seen the fountain in these glimpses, pouring darkness instead of water, and we cannot guess what the visions mean._

Samus went thru the door into the Main Plaza of the Chozo Ruins.

The walls were cracked, crumbling, and overgrown, but the place was still beautiful… and eerie. Samus scanned the leaves of a dead tree. _These leaves appear to be unnaturally dried and withered._ Samus went thru the second door she found because the first had a blast shield over it that she could not destroy, courtesy of the incident on the Orpheon. She went thru a narrow corridor and upon going thru the door at the end, found herself in a hallway with eyons on the walls. These were giant eyeballs made of ocular tissue that fired little lasers as you walked past. Lacking the firepower to dispose of them properly, Samus fired at them to close them briefly.

Thru the door at the end, there was the Ruined Nursery. No, not an infant nursery with insect-bored remains of cribs that once contained baby Chozos, but a plant nursery with a channel set into the wall and a dead tree in one corner.

Samus scanned another shimmering patch of wall.

_We Chozo are departing now, after so many years of peaceful seclusion here on Tallon IV. When we came this place was a refuge for our spirits, a civilization built from native materials, bereft of the trappings of our technology. We were linked to the land here, kindred to the plants and animals, far away from the machines we had become so dependent on. And so we leave it now, pristine, a testament to the mortal forms we no longer need. We have drawn the veils of time and space aside, and are withdrawing beyond the illusion. But we will never forget this, the most sacred of our homes. And we will remain ever watchful._

"Okay, but that still doesn't explain why this place is a wreck," said Samus. She scanned the leaves of the dead tree.

_ Unusually high concentrations of poison identified in tree leaves._ She then scanned the tree itself. _Elevated toxicity levels found in tree bark. Scans indicate a poisoned water source within four meters of tree base._

"Hmm, very interesting," Samus said. After refilling her energy at the nearby station, Samus was attacked by several beelike creatures. The Scan Visor revealed them to be War Wasps. Samus disposed of them, then went thru the door to the North Atrium. All the water there had evaporated. Samus proceeded thru the next door to the Ruined Gallery. There was another door there with a blast shield and more War Wasps. What interested Samus though, were the pipes in the wall pouring out water. Green water.

She scanned them. _These pipes are part of an irrigation system. The source of the water is unknown, but all liquid in this area is toxic._ Samus scanned the pool of water next. _Toxicity levels of this water are very high. Contact with contaminated liquid extremely hazardous._

"Well now I know what they meant by pouring darkness instead of water," said Samus to herself.

The next room was a long corridor. Samus went thru it and arrived at the Hive Totem. It was a creepy place. There was a totem-like metal thing at the back of the room under which was a platform that held a strange glowing object. A dais was in the center of the room, and a bridge stretched from it to the platform with the object. On the walls there were creepy drainages. A moat of toxic water surrounded the dais.

Samus scanned the glowing object. _It appears that this item can only be reached by using the elevated bridge._ Next she scanned the bridge._ This elevated bridge looks worn, but functional._ Then she scanned the metal thing above the platform._ Mechanical device appears to be inactive. Lifeforms detected within hollows of machine._ Samus stepped onto the bridge.

It was a trap.

The moment she put one foot on the bridge, the mechanical device came to life and melded with the platform. The drainages poured forth toxic sludge until the entire room was filled up with toxic water, with only the very top of the dais and Samus above water.

A hatch on the metal thing opened and out came three Ram War Wasps. After scanning them, Samus scanned the metal thing.

_ Morphology: Hive Mecha. Mechanical security unit that's programmed to work with predatory hive dwellers. A design flaw makes the shielding on Hive Mecha weak around their access ports. These units are second-generation combat drones, able to interface with organic units on a higher level. They train, shelter, and work hive-dwelling predators. Unarmed, they rely on their hive beasts to handle any threats._

Samus shot down the wasps. After that, the hatch on the Hive Mecha opened and emitted a red light. Samus scanned it._ Device is emitting a high frequency signal. This may be the cause of the war wasp swarms._ Samus fired in the open port. The port closed and opened again. Out came six Ram War Wasps. Samus shot them down and the process repeated itself once more with nine Ram War Wasps. After that, the water level lowered back to normal, the Hive Mecha raised itself up, the platform was lowered, and a voice said, "Congratulations, Hunter. You have passed the test. You may now access the Missile Launcher."

Samus could hardly believe her ears. "A _test?!_ That whole thing was a _test?!_"


	3. Chapter 3

Chapter 3

Magmoor and Phendrana

The Magmoor Caverns were an area of intense heat and magma not unlike Norfair. It was also home to its namesake, the Magmoor. Upon walking to the edge of the lake, Samus saw a Magmoor rise up out of the lava and breathe fire. Samus blew its head off.

After traveling for a few minutes, Samus came upon the Monitor Station. This was obviously made by the Pirates. Samus got a couple missile expansions and an Energy Tank, then took a nearby elevator to the Phendrana Drifts.

The Phendrana Drifts were the opposite of the Magmoor caverns. Whereas the Magmoor Caverns were an area of intense heat and magma, the Phendrana Drifts were an area of snow, ice, and subzero temperatures. As Samus looked out upon the Phendrana Shorelines, she realized what a wonderful respite it was from Magmoor.

After refilling at a nearby station, Samus headed up until she came to some frozen ruins. There, Samus found another lore entry and scanned it.

_ None know if our temple, the Cradle, will prove powerful enough to contain this abomination forever. How can we Chozo hope for it to remain intact when that which it guards writhes in the darkness, growing always stronger? The fate of this world rests with the gathering of the artifacts we call the Cipher, but even it is not all-powerful. It is strong, yes, an enchanted whole of twelve links. Still, it is finite in its reach and we who guard it are slowly succumbing. When our vigilance crumbles away into madness, the Cipher will be exposed and the fate of Tallon IV will be beyond our influence._

Samus bowed her head, troubled by what she had just read. "Samus," said the Hive Mecha, "the Boost Ball is in the room ahead. Once you get it, you can get the Space Jump Boots."

Samus got the Boost Ball, then went back to the Tallon Overworld and got the Space Jump Boots, allowing her to double jump.

Along the way, she found another lore entry.

_Many Chozo have gone beyond now, and this is a mercy. Those who remain suffer in dimensional flux, drifting helplessly across time and space, guided by unseen and inexorable currents. The Chozo who cling to sanity fight the tide, but our minds are weakening. Soon we will all be like the Turned, Chozo who have been utterly corrupted by the Great Poison. The Turned still hold to their Chozo forms, but their minds are black with fell intentions. Gone is their respect for life. They honor only destruction, and seek to disrupt the artifacts holding the Great Poison at bay. All life taunts them, and they do not rest. Before long, they will be all that remain of the Chozo here._

After refilling at her ship, Samus traveled to the Chozo Artifact Temple to get the first artifact, the artifact of Truth. When Samus grabbed it, she was able to scan clues to the locations of the other artifacts on the totems.

_Invaders have claimed Phendrana as their own. A tower sits atop their fortress. Collapse it to reveal the chamber where the artifact of Elder is held._

_A tall cave stands at Phendrana's Edge. Seek the unseen entrance at it's top to find the artifact of Spirit._

_The heat of Magmoor was a test for many warriors. A shrine in their honor holds the artifact of Strength._

_ Within the ruins of our home, we honor our fallen elders in a great hall. A chamber beneath the statue holds the artifact of World._

_ A sunchamber high atop our ruined home became the nest of a great beast, and a source of corruption. Many Chozo spirits have been drawn to this tainted place. Release their bond to the world to claim the artifact of Wild._

_ There is a tower within the ruins where light always shines. Move thru the waters there to find the artifact of Lifegiver._

_ In one of Tallon's far corners, a grove of life lies. Reveal the pillar beneath the waves to find the artifact of Chozo._

_ Deep within Magmoor a fiery lake lies. Break the pillar at it's center to find the artifact of Nature._

_ Near Phendrana's shorelines, a temple lies. Melt the waters flowing from the elder to find the artifact of Sun._

_ A room of research lies in the mines. A corrupted invader is trapped there. Defeat this creature to earn the artifact of Warrior._

_ Invaders mine the depths in their greed. Roll thru a tunnel of the Great Poison to find the artifact of Newborn._

Samus got the artifact of Strength, then headed to the Phendrana Drifts to get the Wave Beam.


	4. Chapter 4

Chapter 4

Infiltrating the Space Pirate Facility

Samus arrived at the chapel of the elders. At the far end of the room was a pedestal, and on the pedestal was the Wave Beam.

Samus ran toward it, but the pedestal sunk into the floor and four baby Sheegoths attacked.

Baby Sheegoth

Though babies, they were as big as a tiger, and Samus had a tough time taking them down. Despite their big teeth, their backs were vulnerable once the ice was blasted off. But when all four babies were down, the wall at the far end of the room exploded to reveal the last thing Samus wanted to see: an adult Sheegoth.

Adult Sheegoth Fighting the Sheegoth

The size of a siege tank, this thing could kill humans like a terrier killed rats. But it had one big weakness: its belly. Samus rolled into Morph Ball form and dropped bombs underneath the big lug until it was dead.

Samus grabbed the Wave Beam from the pedestal. The Wave Beam was a powerful electric beam with an awesome homing capability. It could also destroy those annoying bombus.

The Wave Beam

Samus left the temple and headed for the ice ruins west. Once there, she went thru the purple door into the ancient courtyard, and solved a puzzle to get up to the top. After filling up at a nearby station, Samus embarked on her mission to infiltrate the Space Pirate base.

Samus killed a Pirate guard and blew up a turret in the hallway, then entered the reception area. But then a drone spotted her and sounded the alarm. The doors locked and a steady stream of Pirates came out to defend the lobby.

Samus wasted no time. She used missiles and charged wave shots to off the Pirates. Samus enjoyed hearing them scream.

After downloading a map of the facility, Samus went to Research Lab Hydra. The Hive Mecha alerted Samus to a new upgrade. "Samus, the Thermal Visor is in the Energy Core. I'm uploading the coordinates now."

After killing the Pirates in the lab, Samus scanned the computers to gain a wealth of information on their operation. The first one said:

_ Scans of the Spiral Sector detected a massive energy spike emanating from a wanderer-class planet known as Tallon IV Scout reconnaissance was immediately dispatched to the center of the spike, a land mass at heading mark 40.08.02, returning with planetary samples and atmospheric imaging. Analysis shows the energy source to be an unstable radioactive material of enormous potential. We are unable to form an accurate risk-assessment at this time, but we are unlikely to find an energy source this powerful again. Analysis will continue, but currently Tallon IV seems to be a viable secondary headquarters._

_We have codified the newfound energy source as Phazon, a V-index mutagen of which we have very little reliable data. Indications point to a meteor of unknown origin impacting approximately 20 years ago, expelling Phazon into the environment. This material seems to possess almost lifelike characteristics, mutating life forms strong enough to withstand its poison. These mutations appear promising, with abrupt evolutionary leaps appearing in single generation reproduction. Plans to establish a full science team on Tallon IV are being finalized._

_Mining operations have begun near the crater where Phazon appears to be the most concentrated. Daily Phazon yields have increased 44%, and our mining system becomes more streamlined as personnel and equipment flows increase. Several incidents of Phazon induced madness have been reported, prompting augmented life support systems in the deeper chambers. Symptoms include loss of equilibrium, erratic respiration, muscle spasms, and in the most extreme cases, hallucinations. Apparently the material is more unstable than initial analysis indicated._

_Phazon mining is under way. Several garrisons have been established, and terraforming of the Chozo Ruins is under way. The Phendrana Drifts have proven too be an optimal location for research headquarters, and soon it will be joined by a combat base and starport. If Command's predictions are half true, we shall rise to dominance in this sector within a deca-cycle. Truly, these are glorious times._

_Oh brother, _Samus thought.

_ Outpost Glacier One in the Phendrana Drifts region of Tallon IV's mountains is operating at 85% capacity. Subzero temperatures have made the Metroids sluggish and easy to control, even those well into Phazon infusion cycles. Cold containment stasis tanks are sufficient for the juveniles, but some of the larger Metroids have been moved to quarantine caves for safety purposes. Security doors remain an issue, as malfunctions due to ice occur every day. Predators are also a concern, but we cannot kill all of them without a vast increase in munitions and soldiers._

_Our tests exposing parasites to Phazon have been quite successful. Increases in strength, size, and aggressiveness are common it all test subjects as well as unforeseen evolutions like poison sacs in the abdomen and a second ring of mandibles in several subjects. These creatures were chosen because of their resilience, and it appears possible that, given enough exposure to Phazon, they may one day be able to survive on any planet we transport them to. Our methods will have to be refined: we currently have a 100% extinction rate after the fourth infusion period, and most of the ones who survive the third one are so violent and uncontrollable that they have to be euthanized. Even so, we remain hopeful that further experimentation will result in success._

Samus left the lab and headed to the Observatory. After restoring power to the holoprojector and grabbing the Super Missile, Samus went to the control tower, then continued to research lab Aether. Some areotroopers blocked the way, but Samus was an old pro at killing them by now. Speaking of old, in a stasis tank in lab Aether, Samus saw an old friend: a Metroid. After she scanned it, the Metroid broke out of it's tank and attacked. Samus blew it up with a super missile.

The Pirates noticed her, but she killed them all. Once they were dead, she scanned the computers to get more data.

_The reconstruction of Ridley was successful. After his defeat on Zebes, Command ordered a number of metagenetic improvements for him. Early tests indicate an increase in strength and offensive capability. We believe our creation, now called Meta Ridley, will become the mainstay of our security force, a job he will certainly relish._

_Confidence is high regarding Phazon applications. We know enough about Phazon now to begin combining it with Space Pirate DNA. The code name for this venture will be Project Helix. Studies indicate Phazon could produce radical new pirate genomes. Phazon madness is a concern, but refinements in the infusion process should reduce or neutralize the odds of mental degeneration._

_Metroid dissection continues to provide more questions than answers. Our research teams have isolated the energy conduits that ran from the invasive twin mandibles to the energy core in the creature's quadripartite nucleus, but the manner in which a Metroid actually extracts the life force from it's prey remains an utter mystery. The victim does not lose blood or any other vital fluids and yet the Metroid extracts energy. Identifying this energy is the key problem. It takes no physical form, and yet without it, the victim dies. We shall continue to research this matter, as the isolation of this life giving essence could be the key to our ascendance._

_Studies of Metroid biology continue, although with limited progress. It seems likely that we will be far more successful using the Metroids of our means rather than trying to reproduce their powers. If they could be adequately tamed, we would have no need of a proper understanding of their metabolism. A small force of disciplined Metroids could wipe out entire armies, and once we find a way to shield them from cold containment weapons, they will be invincible. Furthermore, if we could then harvest the energy they'd consumed, we would have a near limitless source of power at our disposal._

Samus stole the thermal visor from the Pirates, then got out of the base and refilled at the nearby station. The Hive Mecha commed in. "Samus, that 'project titan specimen' you read about sounds pretty dangerous. Maybe you should go and destroy it." Samus went to the quarantine cave. There she found a huge pile of enormous boulders As she walked toward the pile, she heard something. Samus turned around and saw a small rock floating in the air. Then she heard a bigger sound behind her and looked back at the pile of boulders.

The boulders were moving.

Samus watched in horror as Thardus, the geologic monstrosity, stood up and roared to life.

Samus used the Thermal Visor to see one of the boulders, then shot away the outer cover. She then switched back to the combat visor and fired a super missile at the exposed boulder. Thardus roared in agony. Samus repeated the process, eventually destroying the center boulder that was his body. Thardus groaned and toppled to the ground.

Samus felt something hit her head. It was the rock she had seen. Samus kept it as a trophy, and grabbed the Spider Ball from the remains of Thardus. After heading to the Magmoor Caverns, Samus went to the Chozo Ruins to get some more upgrades.


	5. Chapter 5

Chapter 5

The Newborn Grows in Strength

Samus went thru the ruins entrance to the main plaza. "Samus, after you get those two expansions, go to the Sun Tower and use the spider ball track to get into the Sunchamber, where you fought the plant boss." "Roger that, Hive Mecha, I'm on my way," said Samus.

When she arrived at the Sunchamber, the room darkened. Three glowing forms that were shaped like Chozo descended and attacked. Samus knew these were the Turned, Chozo who had been utterly corrupted by the Great Poison. The Turned looked like Chozo, but their minds were black with fell intentions. Gone was their respect for life. They honored only destruction. Samus scanned then and found out that they were immune to fire, ice and electricity. That would mean that her Wave Beam could not harm them, nor could the Ice or Plasma Beams if she had those. Even her missiles did not work. That left only the Power Beam. Rather than using charged shots, Samus used the Super Missile, knowing that an enemy vulnerable only to a certain Beam was also vulnerable to the respective Charge Combo. A super missile was all it took to kill a ghost.

Unfortunately, Samus could only fire when they attacked, for that was when they were visible. Without the X-Ray Visor, it took her a long time to kill them. When the last one died, The artifact of Wild was revealed. Samus grabbed it and headed to the Gathering Hall.

Samus used the Spider Ball track in the furnace to get to the main room of it. There she found a lore entry and scanned it. Samus wept as she read of the plight of those whose blood she shared.

_ The cries of this dying land pulled us from our dreaming state and now we Chozo walk as ghosts while the Great Poison sinks into the trees and waters, devouring all life. Some plants and animals survive, but their forms grow as twisted and evil as the force that fell from the sky. The heart of this planet will succumb soon, and so will we, even in our ghostly states. Already many Chozo have faded and passed into the unknown. The Great Poison is unlike anything we have glimpsed in this or any dimension. It eats relentlessly, worming out life wherever it blooms and corrupting what it cannot kill. It will be our undoing. Our last hope lies in the Cradle, the temple we hope might contain this abomination. It is almost complete, hovering over the impact site, the dark heart of the spreading evil. If we can finish before the last of our kind drifts into madness or death, there is a chance for this world. If we fail we are doomed with it._

Samus reached the Crossway, an eerie room with sunlight coming in thru the ceiling.

Samus boosted up the half-pipe and scanned three new lore entries.

_A second plague has come upon the land, dousing the last flickering hopes of our race. Drawn by the very force we Chozo had hoped to contain, a host of marauding creatures descended from space and invaded our temple, the Cradle. They try in vain to destroy it, but it's power remains beyond them for mow. They possess some of the artifacts we call the Cipher, yet do not comprehend their function. Ignorant creatures, they are blinded by delusions of harnessing the Great Poison for their own designs. They walk about as masters of the planet, assimilating the ruins of our sanctuary into their experiments. We can but watch and wait for our doom._

_The Hatchling walks among us. Are these dreams? Memories? Foretellings? Time and reality swirl together like estuary waters and we Chozo know not what to believe. She appears as ghostlike as the Chozo, but at times the mists clear. We see her wounded eyes, and remember the child we found so long ago. What has she become, this Newborn? Clad in Chozo armor, wielding weapons our hands once held, does she long for the Chozo as we once were? Does she long for her parents, lost to the same creatures that even now defile our sacred home? Does she still live?_

_The prophecies tell of the coming of the Worm. Born of parasites, nurtured in a poisoned womb, the Worm grows, devouring from within, until the world begins to rot. The words of the seers have come to pass, for there, in the depths of the world, the ravenous Worm lurks and feeds. From the stars it came, blighting Tallon with its Great Poison. We can but watch as the Worm grows, watch and wait. For the prophecies also speak of a great Defender, the one who delivers the world from evil. Is the Newborn the defender of which the seers spoke? We shall do all we can to aid her, for she bears our legacy as she bears the ancient armor and weapons of our people._

Samus advanced down the corridor adjacent to the Crossway, arriving at the Hall of the Elders. There she found a Missile Station and refilled her launcher. After killing a ghost, Samus retrieved the Ice Beam from the Antechamber next to the Reflecting Pool and returned to the Hall of the Elders to get an energy tank. Then she used a nearby elevator to return to her gunship in the Tallon Overworld, scanning a lore entry on the way out.

_More and more, or tormented minds turn to the Newborn. As the world continues to shift indo brutal, disconnected images she remains inarguably real, a strong figure delving deep into this blighted world, unmindful of the terrors that await her. Was she this way before? When we Chozo found her, a fledgling orphaned on a savaged planet, did a warriors pulse already beat in her veins, filling her with righteous fury? Our hopes lie with her. We leave these messages for her, that she may find our artifacts and deliver the world from its evils. Wraiths we may be, but our reach is still long indeed. We shall fight the invaders, and the poison they would master, until the end._

Samus saved at her gunship. "Samus," said the Hive Mecha, "In order for you to investigate the wrecked frigate, you must first get the Gravity Suit. It will allow you to move and jump normally while underwater."

Samus traveled to the deepest part of the Phendrana Drifts and got the Gravity Suit, then traveled thru the wrecked frigate. Beyond there she found an elevator to the Phazon Mines. "It's time to infiltrate the bastion of the Pirates," said the Hive Mecha. "I'll give you more instructions when you get there." Samus took the elevator down and arrived at the Phazon Mines.


	6. Chapter 6

Chapter 6

Down to the Phazon Mines

Samus entered the main quarry. Upon her arrival, she received a report from the Hive Mecha. "Samus, the Pirates have stolen your Power Bombs. It's time for you to get them. I am uploading the location of them now."

Samus ascended a ramp, and the pirates noticed her. "Dang! They've spotted me!" "Samus, quick!" said the Hive Mecha. "Kill them before they can get a message to Central Command!"

Samus froze the Pirates with the Ice Beam, them shattered them with missiles. "Well done, Samus. Not a murmur on Pirate channels," said the Hive Mecha.

Samus traveled thru the next few rooms, arriving at Elite Research. She would later use the Power Bombs to release the Phazon Elite, who she would kill to get the Artifact of Warrior.

But for now, Samus just lowered the platforms and scanned a nearby data entry.

_Initial Project Helix experiments with Space Pirate embryos were disastrous. The Phazon infusion process degenerated brain tissue even as it augmented muscle mass. None of what we have termed "Elite Pirates" lived to maturity; the few that survived their infanthood suffered severe psychotic breakdowns as juveniles, killing anything within their zone of perception. Research team Sclera made a recent breakthrough, in which parasite studies with a unique Phazon strain code-named "Vertigo" were highly successful. Since then, we have fused Vertigo Phazon with Space Pirate DNA with great success. The latest batch of Elite Pirates have reached maturity successfully and are ready for field testing and training._

"Well so much for refinements in the infusion process reducing or neutralizing the odds of mental degeneration," Samus muttered.

Samus descended to the second level of the Phazon Mines. There she found another entry.

_Test subject z-d, hereafter referred to as Metroid Prime, was recently discovered in a cavern by mining crews. It quickly dispatched the miners but was eventually contained by security units and drones. Once contained, we were able to begin studies upon Metroid Prime. The results have been astonishing. It is genetically similar to Metroids, albeit on a highly evolved level. It displays a limitless capacity for Phazon infusion and shows no Phazon based degeneration whatsoever. It continues to grow in size, and while it has manifested some psychotic behavior, the cold fields we use to pacify remain effective. Authorization for advanced studies upon Metroid Prime has been approved._

Samus wondered if the Metroid Prime was the Worm that the Chozo had spoken of.

Walking into the room, Samus saw a stasis tank. It broke with a crash, and an Elite Pirate challenged Samus.

Concept art drawing of an Elite Pirate

Samus fired a Super Missile at it, which sent it staggering backward. A second killed it and short-circuited the nearby force fields.

After killing the nearby pirates who had been alerted, Samus scanned another lore entry.

_Science Team is attempting to reverse-engineer Samus Aran's arsenal, based off of data acquired from her assaults on our forces. Progress is slow, but steady. Command would dearly enjoy turning Aran's weapons against her. We believe we can implement Beam weapon prototypes in three cycles. Aran's power suit technology remains a mystery, especially the curious Morph ball function. All attempts at duplicating it have ended in disaster: four test subjects were horribly broken and twisted when they engaged our Morph Ball prototypes. Science Team wisely decided to move on afterward._

The corner of Samus's mouth twitched and she chuckled. Unable to contain herself any longer, she burst into a fit of laughter.

At the top of the room, she found more entries.

_Subject Metroid Prime's breach has been contained. Reports indicate that it sensed a large batch of raw Phazon in the lab from within its stasis tank and broke thru the glass, using previously unsuspected strength. Besides consuming all of the Phazon, Metroid Prime assimilated several weapons and defense systems from fallen security units. It has suffered no ill effects from said assimilation: indeed, it began to use its newly acquired weapons against us. Once we pacified it, we were unable to remove the assimilated gear without threat to Metroid Prime; the gear is now an integral part of its body. Command is intrigued by this newfound ability and has ordered further study to commence at once._

The next one said:

_Metroid Prime continues to feed and grow ever larger in the impact crater caves. Its hunger knows no bounds, and it has begun to manifest some unusual mutations since its breach. These include armor plating on its epidermis and mechanical outgrowths that generate defense screens. These screens render it invulnerable to most weapons, but a flaw in the mutation leads to an increased vulnerability to a certain weapon type. It compensates for this by shifting the screens quickly. This latest development concerns security units greatly; they feel it's only a matter of time before Prime corrects this difficulty and renders it invulnerable to all weaponry. Containment would be nigh on impossible if this were to occur._

More and more, Samus got the feeling that this was the Worm. After going to Omega Research, Samus scanned another entry, just as disturbing.

_Elite Pirate Upsilon's propensity for Phazon has allowed us to infuse it far beyond our safety restrictions, and the results have been extremely encouraging. It shows dexterity with all weaponry, including the chameleon manta issued for cloaking purposes. It displays remarkable healing abilities: when injured, it seeks out Phazon and coats itself in the substance, which instantly mends the creature's wounds. We believe our creation, which we are naming Omega Pirate based on these developments, will be a great asset. Our only concern at this point is its potential overdependence on Phazon._

"Samus," said the Hive Mecha, "I think you're going to have to kill that thing soon." "I agree," said Samus grimly.

After getting the Power Bombs and using one to destroy the Central Dynamo, Samus went back to the first level of the Phazon mines and got the Grapple Beam, the last of the upgrades she had lost on the Orpheon. After taking a quick trip to the Tallon Overworld to get the X-ray visor, Samus cleared out the Magmoor Caverns and the Chozo Ruins, getting the last beam weapon, the Plasma Beam, in the process. Then Samus headed back to the Phazon Mines to confront the Omega Pirate.

The Plasma Beam


	7. Chapter 7

Chapter 7

A Miner Problem

Samus headed back down to the Central Dynamo. This time though, the base was on full alert. Samus found herself having to deal with more and more Pirates as she went thru the Phazon Mines.

Samus soon found herself in Metroid Quarantine A. There, several Pirates were walking around tending the PCs, with a force field behind which were several Metroids. Samus scanned one of the computers to lower the force field.

Immediately, the freed Metroids began to suck on the Pirates in the room. "Surprise!" said Samus. She laughed uproariously as the Metroids feasted on their helpless victims. Once they were done, they turned their attention to Samus, but the Ice Beam and a few missiles but an end to that. Samus crossed the room and took the elevator down to the third level of the Phazon Mines. After hopping on the massive mushrooms in Fungal Hall A, she found herself in the Phazon mining tunnel.

"Samus, the artifact of Newborn is down there, but that area is saturated in Phazon, so you'll die if you try to get it. You need a new suit that will protect you from Phazon." "A new suit?!" said Samus. "Well where the heck am I gonna get a new suit?!" "Don't worry, I'm working on it," came the reply. "Just continue and find the Omega Pirate."

In the Elite Quarters, Samus finally found the Omega Pirate. It soon saw her and smashed the tank, bellowing its challenge for all to hear. The Omega Pirate was almost as tall as Thardus, and just as intimidating.

Samus found that she had to destroy the blue "muscles" on the monster's arms and legs in order to get it to cloak. One Super Missile was all it took to destroy one. After all of them were blown off, the Omega Pirate vanished and called in several troopers. Samus eliminated them and switched to the X-Ray Visor. When the Omega Pirate positioned himself over one of the deposits of Phazon to regenerate his armor, Samus fire a super missile straight at his chest.

The bug lug doubled over and ran over to another pool of Phazon. While it tried to heal itself, Samus fired another super missile into it, causing major damage. In the end, it had to fight without haling itself, just restore its armor. Samus blew it off and when it cloaked, she fired another super missile at his chest. One more Super Missile was more than he could take, and the mighty one toppled to the ground.

Once killed, the Omega Pirate literally did topple to the ground, and right onto Samus Aran. Bubbling, the corpse dissolved into pure Vertigo Phazon. The Phazon seeped into her suit, turning it black. Purely by accident, Samus had acquired the Phazon Suit.

Phazon Suit

"Excellent job, Samus Aran," said the Hive Mecha. Now get that artifact and let's get out of here!" Samus retrieved the artifact, then went to the Phendrana Drifts to get the remaining three. With that job done, Samus could at last unite them at the Cradle.


	8. Chapter 8

Chapter 8

Returning the Artifacts

Samus returned to the temple and set the artifacts in place. Together they opened up a portal to the crater. Then she heard a familiar sound. Next minute a long tail smashed into the portal, destroying it. Samus did not need to look up to know it was Meta Ridley.

"Surprise!" said Ridley. As Samus glared at him, the space dragon said, "I have to admit, Science Team had to spend a lot of time getting me ready to fight you, but man… I wasn't good enough! After you trashed me last time, they had to make some major modifications!"

"I don't care what modifications they made," Samus hissed. "I beat the crap out of you once, I can beat the crap out of you again." "We'll see about that," said Ridley. And the battle began.

Ridley fired a laser from his mouth and launched missiles at Samus. Samus locked on and fired a Super Missile straight at his chest, knocking him backward in midair screaming. After firing two more, Samus watched as Ridley flew around and dropped bombs, destroying the totems. When he landed in the center of the temple, Samus fired another super missile at his chest.

Eventually, Ridley's wings were set aflame and blew up, rendering them useless. Ridley landed on the temple for the next fight.

Now he reared back and lunged forward, slamming into Samus. He repeated the process several times, and Samus tried desperately to get away from him, but in vain. She saw her opportunity when Ridley paused to breathe fire. Samus fired a charged shot into his mouth, sending him staggering backward, exposing his chest. Samus fired a super missile into his chest, dealing heavy damage. As Meta Ridley staggered back and screamed, the eyes of the Chozo heads on the temple turned red. Firing lasers, they shoved the winged beast off the edge of the temple and down into the impact crater, hitting the bottom four thousand feet below with a resounding thud.

Samus turned and saw twelve Chozo ghosts open up the portal. One of them turned to her and said, "Thank you, Hatchling. We have reopened the portal. Now go and finish the job."

Samus stepped into the portal and found herself in a small room with an energy station. Samus refilled and stepped thru the red door deep into the impact crater.


	9. Chapter 9

Chapter 9

The Worm Unleashed

Samus looked out upon the Phazon core. It was a massive room with a huge pillar in the center. Samus saw and scanned a Phazon Metroid,* the second and final Phazon variant of a Metroid.** After refilling at the nearby missile station, Samus entered a tunnel leading to the door to a large room. The source of all that was ill with Tallon IV was on the other side of that door, and it was about to unleash a fury never before seen by Samus or anyone else. On any planet.

In the room there was what appeared to be a giant head hanging from the ceiling. However, what looked like a mouth and eyes turned out to be just markings. As Samus watched, several legs uncurled. Red eyes opened. And a huge black spider landed on the floor and burrowed a hole thru the far wall. Samus knew it was the Worm. The Metroid Prime.

Samus jumped down into a small chamber. The spider changed the color of its markings from white to yellow. Drawing upon knowledge gained by reading the Pirate entries, Samus fired a Super Missile right between the eyes. The thing lifted up and fired a yellow laser from an opening on its underbelly. After getting hit by another super missile, Prime lunged forward and swung a leg at Samus, changing its color to purple while doing so. Samus charged up the Wave Beam and gave it a taste of the Wavebuster charge combo that she had gotten in the Tower of Light.

After getting several hundred gigajewels of electricity pumped into him, Prime burrowed thru the floor into another chamber. This time, after Samus dished out damage, Prime charged to try to bowl Samus over with his heft. Samus simply rolled into morph ball form. After repeating this process thru two subsequent rooms, Prime broke thru the wall and slumped over, rolling into a big hole.

Samus jumped down thru the hole and found herself in a large dark room. The lifeless corpse of the Metroid Prime lay there in a pool of Phazon. Then it happened.

From the crumpled body rose a specter unlike anything Samus had ever seen. In the very bottom of the impact crater, the Metroid Prime showed its true form. A glowing blue octopus with six tentacles and two red eyes that glowed brighter still.

2nd form concept art

Anthropomorphic tendencies be damned, Samus thought. Those eyes were irrefutably malevolent.

Samus scanned the thing and learned it was invincible. Samus could not harm it with any of her weapons. The Worm raised its tentacles and slammed them on the ground, creating a shockwave. Samus jumped over it, then watched as the vile creature excreted a pool of pure Vertigo Phazon. When it floated to one side, Samus stepped into the pool. Immediately her arm cannon changed shape, becoming larger and rocky with blue cracks in it. Samus had unlocked the Phazon Beam.

The bounty hunter poured raw Phazon onto the Metroid Prime, a constant stream as the Worm spasmed as if shocked by electricity. The Metroid Prime again squirted out a Phazon pool, but this time also spawned two Metroids!

Samus jumped into the pool and poured raw Phazon onto the Metroids, destroying them instantly. She then turned her gun upon Prime and poured the contents of the pool into it, watching in satisfaction as the creatures spasmed in pain.

Again the Worm made a Phazon pool, but this time spawned two hunter Metroids. Samus killed them with the Phazon Beam, then blasted Prime until the pool was no more. One last time the creature squirted out a pool, with two Phazon Metroids as little guards. Samus shot the annoying critters, then poured the contents of the last pool into the Metroid Prime. When the pool was no more, Samus stopped.

The Metroid Prime shuddered. It shuddered and shook and trembled violently. Finally it changed from an octopus into a round blob with short appendages. Two of these shot out, one latching onto Samus, the other onto her arm cannon. A tug of war ensued, resulting in the Worm letting go. When it did, Samus saw that her Phazon Suit was gone, leaving only the Gravity Suit.

The Metroid Prime swelled. It grew bigger and bigger, stretching tighter and tighter. It was like a big balloon being inflated. Samus knew it would explode and turned and ran. As the Worm died behind her, Samus rode the explosion up and out of the room.

_Crater collapse imminent. Evacuate immediately._

Samus used the portal to the artifact temple. The temple floor burst into flame. Samus signaled her ship and jumped over the edge. The ship picked her up and Samus stared at the burning temple.

Samus took off her helmet and looked out upon burning Cradle. Great joy filled her heart. "I did it!" she said. "I slew the Metroid Prime! Tallon IV is saved!" Looking at the Chozo heads, she said, "Chozo, I have avenged you."

Samus got in her ship and said farewell to the Hive Mecha. As it wished her well, she thought of Adam, and how much she missed him. Ignoring the ache in her chest, Samus left Tallon IV and blasted into hyperspace. Mission Accomplished.

*Author's note: the Phazon Metroids are from prime 3 there really are Fission Metroids here, which after you shoot them split into two Metroids of different colors, with the color indicating the beam to blast them with. I omitted the Fission Metroids and replaced them with Phazon Metroids from Prime 3 because I think they were an unnecessary gimmick. I also have omitted the pink Phazon in the impact crater for the same reason, as it was just a throwback to Super Metroid where the gravity suit protects you from some but not all lava, unlike the other 2-D games where it protects you from all. So it was a stupid gimmick.

**The first is the Hunter Metroid which I did not bother to mention in the story. So the order of evolution with Metroids exposed to Phazon is: MetroidHunter MetroidPhazon Metroid. (Actually fission in this game; see above.) Aside from the Phazon variants, unknown elements in the ecosystem of the homeworld of the Metroids, SR388, cause them to evolve into other forms, but that's another story.


	10. Chapter 10

Epilogue

Deep beneath the impact crater, in the room where Samus had fought the Metroid Prime, a single pool of Phazon remained. The pool bubbled and frothed like a smoothie.

A hand reached out of the pool. A metal hand. A hand that clenched and unclenched, grasping at the air. Looking for food.


End file.
